New: CloudBioLinux packages are now listed on biogems.info !

# biogem description by cite version released stars issues source build total 90d*) 7d   90d**)
downloads commits
bio
Bioinformatics library !
BioRuby project
3 months
302
14
128381
0
1
Parser of scientific names !
Dmitry Mozzherin
15 months
23
3
74095
0
0
Binder of samtools for Ruby, on the top
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
4 weeks
23
6
55306
0
23
Biogem is a software generator for Ruby in !
Raoul J.P. Bonnal, Pjotr Prins
2 years
15
12
51214
0
0
Blast search made easy! !
Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.
2 weeks
106
50
43127
0
12
Gadgets for bioinformatics
Shintaro Katayama
3 years
1
37091
0
0
The Ruby ucsc api: accessing the ucsc genome !
Hiroyuki Mishima, Jan Aerts
2 years
16
1
34742
0
0
Http requests to entrez e-utilities
Jared Ning
19 months
7
1
32106
0
0
Create pretty svg-format images of features, gene models
Dan MacLean
2 years
13
5
30082
0
0
A Ruby api for interacting with biomart services !
Darren Oakley
5 years
18
5
29003
0
0
Maf parser for BioRuby
Clayton Wheeler
4 years
10
36
25492
0
0
Gff3 parser for big data !
Pjotr Prins
4 years
6
2
24479
0
0
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer !
Pjotr Prins
19 months
12
1
23156
0
0
A biogem to submit jobs on a queue
Francesco Strozzi
4 years
5
...
22526
0
0
Interfaces with biomodel search engine !
Niall Beard
4 years
1
...
21960
0
0
Tool to work with polyploids, ngs and molecular
Ricardo H.  Ramirez-Gonzalez
16 months
1
1
20680
0
5
Log4r wrapper with extra features for roles and !
Pjotr Prins
4 years
4
2
19847
0
0
An open source framework for transforming heterogeneous data
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
23 months
12
3
19009
0
0
A simple obo file handler !
mjy
5 years
5
...
18800
0
0
Swiss army knife of tabulated data; transforming/filtering tab/csv
Pjotr Prins
2 years
9
20
16339
0
0
Data mining algorithms for jRuby
arrigonialberto86
3 years
16
3
15889
0
0
Support for multiple sequence alignments (msa)
Pjotr Prins
8 weeks
9
5
15812
0
5
A fast parser for fastq files
Francesco Strozzi
4 years
10
...
15555
0
0
A tool to classify and manipulate pfemp1 dbl-alpha
George Githinji
3 years
13055
0
0
Low memory sequence emitters
Pjotr Prins
2 years
11
1
12587
0
0
Pipeline to remove contaminations from est libraries
Philipp Comans
5 years
2
1
12370
0
0
A wrapper for the signal peptide prediction algorith
Ben J Woodcroft
2 years
3
...
12065
0
0
A nexus file format (phylogenetic inference) parser in !
mjy
5 years
1
...
11676
0
0
Fast multi-purpose multi-threaded vcf parser
Pjotr Prins
10 months
38
8
11652
0
0
Build genome output files
Michael Barton
3 years
7
...
11551
0
0
A biogem for counting small kmers for fingerprinting
Ben J Woodcroft
3 years
5
...
11258
0
0
Bio-ngs provides a framework for handling ngs data
Francesco Strozzi, Raoul J.P. Bonnal
4 years
30
15
11103
0
0
A BioRuby plugin for interaction with the transmembrane
Ben J. Woodcroft
4 years
2
...
10880
0
0
Simple morphbank (http://morphbank.net) services accessor !
mjy
5 years
1
...
10607
0
0
BioRuby assembly plugin
Chase Miller, Francesco Strozzi
5 years
4
...
10576
0
0
Ruby wrapper for sambamba tool
Artem Tarasov
4 years
2
...
10551
0
0
Rocker
Luis (Coto) Orellana, Luis M. Rodriguez-R
6 months
10489
0
0
Lightweight Ruby api for ncbi eutils
Joon Lee, aka seouri
3 years
8
1
10232
0
0
A BioRuby plugin for calculating the isoelectric point
George Githinji, Pascal Betz
4 years
3
...
10051
0
0
BioRuby plugin for reading and writing nexml (http://nexml.org) !
Rutger Vos, Anurag Priyam
4 years
8
2
10024
0
0
Basespace Ruby sdk is a Ruby based software
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
3 years
13
2
9825
0
0
Supports linking of models within a ror application !
Stuart Owen, Quyen Nguyen
2.2
2 years
...
9638
0
0
Parser to work with file formats used in
Ben J Woodcroft
23 months
...
9010
0
0
Library for visualizing genomic regions !
Jan Aerts
1.4
8 years
21
1
8900
0
0
A BioRuby plugin: handling genomic interavals and overlaps
Hiroyuki Mishima
5 years
4
...
8857
0
0
Server for polymarker. to be used with cron
Ricardo H.  Ramirez-Gonzalez
21 months
...
8842
0
0
Reading/writing bgzf blocks
Artem Tarasov, Clayton Wheeler
4 years
3
...
8745
0
0
Running and parsing of the protein transmembrane domain
Ben J Woodcroft
5 years
1
...
8114
0
0
Read and manipulate cd-hit clusters
George Githinji
3 years
7555
0
0
Identifying problems with gene predictions !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
7 months
1
...
7492
0
0
Ruby binding for bwa mapping software
Francesco Strozzi
5 years
4
...
7457
0
0
Ruby binding for samtools tabix
throwern
3 years
5
...
7393
0
0
A plugin that allows you to parse large
robsyme
5 years
1
...
7206
0
0
Ruby parser for fastqc output
Tazro Inutano Ohta
5 weeks
2
...
7020
0
16
Iterate through a samtools pileup file
Ben J. Woodcroft
4 years
2
...
7006
0
0
Gene ontology (go) interface for Ruby
Ben J Woodcroft
6 years
10
...
6939
0
0
A general purpose framework for scripted handling of development/stable
mjy
3 years
2
1
6845
0
0
Api to ensembl databases !
Jan Aerts, Francesco Strozzi
5 years
41
5
6448
0
0
Retrieve dna sequence from ucsc using given coordinates
Andrei Rozanski
16 months
6425
0
0
Implementation of the plasmoap algorithm
Ben J Woodcroft
7 months
1
...
6322
0
0
Ruby wrapper for the gff3-pltools
Marjan Povolni
4 years
13
19
6262
0
0
Next-generation mapping of mutations
Dan MacLean
4 years
2
...
6162
0
0
Chembl rest api client, parser and container
Mitsuteru Nakao
4 years
1
1
6153
0
0
Ruby binding to the ucsc kent utilities
throwern
4 years
2
...
6074
0
0
Timeseries modules for statsample
Ankur Goel, Claudio Bustos
3 years
6030
0
0
Publish scientific results to the semantic web !
Will Strinz
2 years
3
16
5809
0
0
This biogem is built around krona, a flashy
Ben J. Woodcroft
12 months
1
...
5766
0
0
Bindings to some internals of the velvet assembler
Ben Woodcroft
4 months
1
5717
0
0
Bioinformatics triple-store support
Pjotr Prins
4 years
4
1
5663
0
0
Parse affymetrix cel/cdf files
Pjotr Prins
5 years
2
1
5641
0
0
Geneexpression illuminahumanannotation
Raoul J.P. Bonnal
5 years
1
...
5542
0
0
BioRuby plugin for unichem rest web service
Mitsuteru Nakao
3 years
5305
0
0
Reports whether a nucleotide change results in synonymous
Dan MacLean
3 years
...
5205
0
0
BioRuby core plugins, most and stable plugins. blastxmlparser, !
Raoul J.P. Bonnal
5 years
1
...
4942
0
0
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover)
Andrei Rozanski
2 years
1
...
4878
0
0
Programmatic interface to the cnls nuclear localisation signal
Ben J. Woodcroft
4 years
2
...
4753
0
0
Enables the localisation predictor wolf psort to be
Ben J Woodcroft
4 years
1
...
4749
0
0
Dead simple method of running shell commands from
Ben J. Woodcroft
7 months
...
4656
0
0
A protparam compatible utility for BioRuby
hryk
3 years
2
...
4370
0
0
A web app wrapper for genevalidator !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
2 months
1
...
4366
0
0
Parse pfam hmm definition files
Ben J. Woodcroft
4 years
1
...
4345
0
0
Bio-gag is a biogem for detecting and correcting
Ben J Woodcroft
4 years
2
...
4183
0
0
A pipeline manager
Francesco Strozzi, Raoul Jean Pierre Bonnal
7 months
15
6
3974
0
0
Biostars data-mining and statistical analysis
Joachim Baran
2 years
3687
0
0
Pass a full citation, get the bibtex back, !
Matt Yoder
2 years
1
3660
0
0
Enables parsing of hmmer version 3 reports
Christian Zmasek, Ben J Woodcroft
16 months
2
1
3416
0
0
Client for xoopit's cloudquery api
Cameron Walters, nb.io
7 years
5
...
3324
0
0
Fast storage and comparison of chr+pos(+alt) locations
Pjotr Prins
15 months
2
1
3289
0
0
Gggenome Ruby client
Mitsuteru Nakao
3 years
1
...
3246
0
0
Ruby ensembl rest api
Alberto Donizetti
3 years
3
...
3192
0
0
Rubybhl is a simple request/response wrapper for the !
Matt Yoder
2 years
6
...
3091
0
0
Generalized linear models for statsample
Ankur Goel
3 years
3065
0
0
A sequence read archive (sra) download script and
Ben J. Woodcroft
11 months
3
...
3056
0
0
Hello world plugin for the BioRuby (just for
Toshiaki Katayama
5 years
3
...
2920
0
0
BioRuby plugin for sun grid engine
Toshiaki Katayama
5 years
4
...
2917
0
0
Digests dna based on restriction enzyme cut patterns !
Trevor Wennblom
5 years
1
2869
0
0
Interface for express beta diversity
Ben J. Woodcroft
2 years
...
2865
0
0
Bio-repeatmasker
Andrei Rozanski
2 years
...
2797
0
0
Does high pairwise alignment of sequencing reads with
John T. Prince
6 years
1
...
2794
0
0
A method to get the nucleotide sequence of
Ben J Woodcroft
5 years
1
...
2694
0
0
A parser for cigar format alignments
Ben J Woodcroft
2 years
4
...
2648
0
0
BioRuby core ext: plugins which require external library !
Raoul J.P. Bonnal, Pjotr Prins
5 years
1
...
2632
0
0
Meta package for biolinux distribution !
Raoul J.P. Bonnal
5 years
2
...
2621
0
0
A Ruby api to the ensembl database !
Jan Aerts, Francesco Strozzi
5 years
4
...
2603
0
0
Restriction enzyme dataset !
Sir Richard J. Roberts, Trevor Wennblom
5 years
...
2585
0
0
One-line summary of your gem
Toshiaki Katayama
5 years
1
...
2585
0
0
Helper methods for reading .delta files
robsyme
20 months
...
2574
0
0
Web server for bio-samtools
homonecloco
2 years
...
2572
0
0
Decoding the dbsnp bitfield
Hiroyuki Mishima
5 years
4
...
2544
0
0
Biological extensions for the intermine webservice client library
Alex Kalderimis
5 years
1
...
2540
0
0
Hydropathy scale for BioRuby
Ben J Woodcroft
4 years
1
...
2530
0
0
Phyloxml plugin for BioRuby
Diana Jaunzeikare, Clayton Wheeler
4 years
3
1
2530
0
0
Wrapper around the exportpred algorithm for predicting p
Ben J Woodcroft
4 years
1
...
2527
0
0
A simple biogem that allows computation of the
Ben J Woodcroft
4 years
1
...
2496
0
0
Fast download blast databases from ncbi beta
Anurag Priyam
9 months
5
1
2470
0
0
A programmatic interface to the ipcress in-silico pcr
Ben J Woodcroft
4 years
3
...
2414
0
0
Csshttprequest is cross-domain ajax using css as a
Cameron Walters, Randy Reddig
7 years
89
1
2389
0
0
Build graph with jRuby
Matteo Picciolini
4 years
2325
0
0
Reads metadata from integrated microbial genomes (img) metadata
Ben J. Woodcroft
3 years
...
2076
0
0
Parse stockholm sequence alignment format
Ben J. Woodcroft
3 years
2
...
1895
0
0
Ruby wrapper to run standard-raxml for maximum likelihood
Fernando Izquierdo
3 years
...
1811
0
0
Aggregate fastqc (quality control for next generation sequencing
Raoul Jean Pierre Bonnal
17 months
...
1711
0
0
Emulates as if old BioRuby biofetch alives
Naohisa Goto
5 months
...
1683
0
0
The api for freebayes version #{bio::freebayes::extversion}
Natapol Pornputtapong
18 months
1646
0
0
Ruby inferface for kseq.h by heng li for
Fedor Gusev
2 years
2
...
1472
0
0
Mine publications for gene names
Pjotr Prins
2 years
...
1428
0
0
A Ruby wrapper on the open tree api beta
Matt Yoder
2 years
1
...
1328
0
0
A restful service for sharing genomic data !
Joachim Baran, Robert Buels, Michel Dumontier
2 years
1309
0
0
Tools to work with fasta files, indexed with
homonecloco
2 years
...
1265
0
0
Tools to manipulate blat files from the command
homonecloco
2 years
...
1235
0
0
Faldo location output method for bio::location in BioRuby
Joachim Baran, Naohisa Goto
2 years
...
1204
0
0
Api of picard tool
Natapol Pornputtapong
18 months
1109
0
0
Csshttprequest is cross-domain ajax using css disabled
Cameron Walters, Randy Reddig
0.1
7 years
1054
0
0
A Ruby wrapper for bio sparql service
Natapol Pornputtapong
19 months
850
0
0
A pipeline creator for BioRuby
Natapol Pornputtapong
15 months
825
0
0
Tools for jaspar motifs in BioRuby
Jessica Lee, Wasserman Lab
14 months
...
817
0
0
Basic wrapper for the kallistio mapper
homonecloco
14 months
1
...
792
0
0
Methods for handling multiwell plate annotations
Steve Pettitt
10 months
...
642
0
0
Parsing and mutation calling from sam, cigar and
Stephen Pettitt
10 months
...
584
0
0
Biosql plugin for BioRuby
BioRuby project
5 months
...
342
0
0
pre
pre
...
0
0
0
*) gem downloads (total & last 90 days) from rubygems.org as of 2016-12-08
**) number of commits on GitHub (last 7 days & last 90 days)